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duplicate the variant to create another one with the 2nd position.
What format are your translocations inputted in?
The structure of the VCF is:
chr1 84799235 MantaBND:6124:1:2:0:0:0:0 A A]chr14:85914438] . PASS SVTYPE=BND;MATEID=MantaBND:6124:1:2:0:0:0:1;IMPRECISE;CIPOS=-92,92;SOMATIC;SOMATICSCORE=34;BND_DEPTH=27;MATE_BND_DEPTH=31 PR
@Emily_Ensembl the breakpoint is defined in the ALT column.
A]chr14:85914438]Yes, I can see that.
Sorry, I see now that Manta actually reports breakend translocations on double rows so 'chr14 85914438' comes further down a second row, which means that it gets a gene annotatation by VEP. Sorry, my bad...
no problem, please, close your question.